Mercurial > repos > galaxyp > msconvert
diff msconvert_macros.xml @ 14:3cf310697624 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
| author | galaxyp |
|---|---|
| date | Mon, 16 Nov 2020 17:25:12 +0000 |
| parents | 9b61227976d6 |
| children | 6153e8ada1ee |
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--- a/msconvert_macros.xml Sat Jul 25 18:13:58 2020 -0400 +++ b/msconvert_macros.xml Mon Nov 16 17:25:12 2020 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@VERSION@">3.0.19052</token> <token name="@FULL_VERSION@">@VERSION@-089e81090</token> - + <xml name="msconvertCommand"> <command detect_errors="exit_code"> <![CDATA[ @@ -39,32 +39,29 @@ ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && #end if - uid=`id -u` && - gid=`id -g` && - wine64_anyuser msconvert ${inputmask} + CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) && + if [ "\$CAN_SUDO" -eq "0" ]; then + uid=`id -u` && + gid=`id -g` && + WINE="wine64_anyuser"; + else + WINE="wine64" && + ## create a writable copy of wine prefix (since copying fails for some html + ## stderr and exit code is swallowed) + export WINEPREFIX=\$(mktemp -d) && + (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true); + fi + && + \$WINE msconvert ${inputmask} + --outdir outputs --${output_type} - - #if $general_options.combineIonMobilitySpectra: - --combineIonMobilitySpectra - #end if - - #if $general_options.simAsSpectra: - --simAsSpectra - #end if - - #if $general_options.srmAsSpectra: - --srmAsSpectra - #end if - - #if $general_options.acceptZeroLengthSpectra: - --acceptZeroLengthSpectra - #end if - - #if $general_options.ignoreUnknownInstrumentError: - --ignoreUnknownInstrumentError - #end if + $general_options.combineIonMobilitySpectra + $general_options.simAsSpectra + $general_options.srmAsSpectra + $general_options.acceptZeroLengthSpectra + $general_options.ignoreUnknownInstrumentError #if $general_options.scan_summing.do_scan_summing: --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" @@ -181,8 +178,8 @@ #if str($filtering.analyzer) != "false" --filter "analyzer $filtering.analyzer" #end if - - ## OUTPUT ENCODING + + ## OUTPUT ENCODING #set $mz_encoding = str($settings.mz_encoding) #set $intensity_encoding = str($settings.intensity_encoding) #if $mz_encoding == $intensity_encoding @@ -217,14 +214,21 @@ #if $general_options.multi_run_output.do_multi_run_output == 'false': --outfile '${os.path.splitext($basename)[0]}' - && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}' + && + if [ "\$CAN_SUDO" -eq "0" ]; then + sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' && + sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; + else + mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; + fi #else - && sudo chown \$uid:\$gid 'outputs' -R && ls -la outputs/ #end if #if $data_processing.precursor_refinement.use_mzrefinement - && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement' + && if [ "\$CAN_SUDO" -ne "0" ]; then + mv '$output_refinement_name' '$output_refinement'; + fi #end if ]]> </command> @@ -243,7 +247,7 @@ <option value="ms2">ms2</option> </param> - <section name="data_processing" title="Data Processing Filters"> + <section name="data_processing" title="Data Processing Filters"> <conditional name="peak_picking"> <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" /> <when value="false" /> @@ -407,7 +411,7 @@ <section name="filtering" title="Scan Inclusion/Exclusion Filters"> - + <param name="activation" type="select" label="Filter by Activation"> <option value="false" selected="true">no</option> <option value="ETD">ETD</option> @@ -462,7 +466,7 @@ </section> <section name="general_options" title="General Options"> - <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." /> + <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." /> <conditional name="scan_summing"> <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" /> @@ -474,10 +478,10 @@ </when> </conditional> - <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" /> - <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" /> - <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" /> - <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" /> + <param argument="--simAsSpectra" type="boolean" truevalue="--simAsSpectra" falsevalue="" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" /> + <param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue="" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" /> + <param argument="--acceptZeroLengthSpectra" type="boolean" truevalue="--acceptZeroLengthSpectra" falsevalue="" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" /> + <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue="" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" /> <conditional name="multi_run_output"> <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" /> @@ -514,7 +518,7 @@ <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" /> </section> </xml> - + <xml name="msconvertOutput"> <outputs> <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" > @@ -646,7 +650,7 @@ <param name="pick_peaks" value="true" /> <param name="pick_peaks_algorithm" value="cwt" /> <param name="pick_peaks_ms_levels" value="1" /> - <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> + <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> @@ -736,7 +740,7 @@ <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> </test> - + <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> <param name="license_agreement" value="true" />